This script prepares scores (status and trend) for Iconic Species in each global coastal region. For each iconic marine species, the countries of occurrence are pulled from the IUCN API. Extinction risk categories for each species are pulled based on current and past assessments; by tracking the assessed extinction risk over time, we can understand the trends of extinction risk for iconic species directly rather than using the “population trend” method from prior OHI assessments.
The Iconic Species sub-goal model calculates a region’s status based upon an unweighted average of species health for all ‘iconic’ species found within each reporting region.
From Halpern et al (2012):
Iconic species are those that are relevant to local cultural identity through a species’ relationship to one or more of the following: 1) traditional activities such as fishing, hunting or commerce; 2) local ethnic or religious practices; 3) existence value; and 4) locally-recognized aesthetic value (e.g., touristic attractions/common subjects for art such as whales). Habitat-forming species are not included in this definition of iconic species, nor are species that are harvested solely for economic or utilitarian purposes (even though they may be iconic to a sector or individual). …
Ultimately, almost any species can be iconic to someone, and so the intent with this goal was to focus on those species widely seen as iconic within a country, and iconic from a cultural or existence value (rather than for a livelihoods or extractive reason). …
The reference point is to have the risk status of all assessed species as Least Concern (i.e., a goal score = 1.0)
The Status of this sub-goal (XICO) is then the % of iconic species in each threat category (as defined by the IUCN Red List), such that:
\[X_{ICO} = \frac{\displaystyle\sum_{category}S_{cat}*w_{cat}}{\displaystyle\sum_{category}S_{cat}}\]
where for each IUCN threat category:
ICO trend is calculated in a similar manner, but weightings are assigned according to IUCN population trend: ‘Decreasing’ = -0.5, ‘Stable’ = 0.0, ‘Increasing’ = +0.5.
Changes since 2015 ICO subgoal for global OHI:
List of iconic species:
Species native country information:
Using the IUCN API, we accessed the full IUCN species list at http://apiv3.iucnredlist.org/api/v3/speciescount?token=
iucn_sid | kingdom | phylum | class | order | family | genus | sciname | population | category
The list of Iconic Species is based upon the original ICO list generated in 2011, using species identified as globally iconic (WWF Flagship species and Priority species) or regionally iconic (based upon WWF regional/local priority species and nation-specific lists).
Filtering the complete IUCN species list to include only the identified Iconic Species, we then use the IUCN API to access the list of countries in which each species occurs, from http://apiv3.iucnredlist.org/api/v3/species/countries/id/
For each of these species, use the IUCN API to gather a list of countries in which it is present.
## The following IUCN countries did not match with OHI region names:
## [1] "Czech Republic, Andorra, Afghanistan, Armenia, Austria, Azerbaijan, Belarus, Switzerland, Hungary, Kyrgyzstan, Kazakhstan, Liechtenstein, Luxembourg, Moldova, Macedonia, the former Yugoslav Republic of, Mongolia, Slovakia, Tajikistan, Uzbekistan, Uganda, San Marino"
ico_spp_rgn_prepped saved at ~/github/ohiprep/globalprep/spp_ico/v2016/int/ico_spp_rgn_prepped.csv:
We accessed the IUCN API to determine past IUCN assessments for each of the identified iconic species: http://apiv3.iucnredlist.org/api/v3/species/history/id/
Each assessment includes a year and an extinction risk, along with additional information on the assessment.
These raw assessments are cleaned up to standardize codes and categories, and category scores are assigned based on a scale from Least Concern = 1 to Extinct = 0, as per the Species OHI subgoal. Note that past assessments used different coding, especially prior to 1994; we reclassified older codes according to this chart:
New category <- original category/description
# NT <- "LOWER RISK/NEAR THREATENED (LR/NT)"
# T <- "THREATENED (T)" treat as "EN"
# VU <- "VULNERABLE (V)"
# EN <- "ENDANGERED (E)"
# LR/CD <- "LOWER RISK/CONSERVATION DEPENDENT (LR/CD)" treat as between VU and NT
# CR <- "VERY RARE AND BELIEVED TO BE DECREASING IN NUMBERS"
# T <- "LESS RARE BUT BELIEVED TO BE THREATENED-REQUIRES WATCHING"
# DD <- "INSUFFICIENTLY KNOWN (K)"
# DD <- "INDETERMINATE (I)"
# DD <- "STATUS INADEQUATELY KNOWN-SURVEY REQUIRED OR DATA SOUGHT"
# NE <- "NOT RECOGNIZED (NR)"
Using tidyr::complete() and tidyr::fill(), we create a full time series for all species from the earliest assessment to the most recent year.
Using dplyr::full_join() we combine the ico_spp_rgn dataframe (iconic species by OHI region) with the ico_spp_cat dataframe (iconic species by category and year, with species info, year, and category info).
Sample of ico_spp_rgn_cat saved at ~/github/ohiprep/globalprep/spp_ico/v2016/int/ico_spp_rgn_cat.csv:
| iucn_sid | sciname | year | cat_code | cat_score | rgn_id | rgn_name | comname | ico_gl | ico_rgn_id | presence |
|---|---|---|---|---|---|---|---|---|---|---|
| 2467 | Balaena mysticetus | 2000 | CD | 0.3 | 218 | Canada | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2000 | CD | 0.3 | 145 | Greenland | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2000 | CD | 0.3 | 163 | United States | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2001 | CD | 0.3 | 218 | Canada | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2001 | CD | 0.3 | 145 | Greenland | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2001 | CD | 0.3 | 163 | United States | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2002 | CD | 0.3 | 218 | Canada | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2002 | CD | 0.3 | 145 | Greenland | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2002 | CD | 0.3 | 163 | United States | Bowhead whale | TRUE | NA | Extant |
| 2467 | Balaena mysticetus | 2003 | CD | 0.3 | 218 | Canada | Bowhead whale | TRUE | NA | Extant |
The toolbox wants rgn_id, species sciname, and extinction risk category for the basic calculations. Since some regions contain multiple subpops (or parent/subpop) we also include iucn_sid to differentiate. This information is included for each year, filtered back to the year 2000.
While the official calculations are performed in the toolbox, we perform the same basic calcs here to get a sense of the ICO status and trend ahead of time.
## # A tibble: 0 × 5
## # ... with 5 variables: rgn_id <int>, sciname <chr>, iucn_sid <int>,
## # year <dbl>, category <chr>
##
## CD CR EN EX LC NT VU
## 316 5857 10524 51 8639 8412 12050
To examine results of the new methods (including API-based data scraping and trend based on time series), we plot the estimated status and trend over time.